The air traffic control tower is seen behind the departures level of Terminal 2 at Chicago's O'Hare Airport on Aug. 13, 2013. / AFP/Getty Images

by Bart Jansen, USA TODAY

by Bart Jansen, USA TODAY

The smokey evacuation of an air-traffic control facility near Chicago combined with thunderstorms Tuesday to disrupt nearly half the flights at O'Hare airport and nearly one-third at Midway airport.

The Federal Aviation Administration said a faulty heating-and-air-conditioning motor sent smoke through the air-traffic control facility in Elgin, Ill., and prompted the evacuation about 12:30 p.m. ET.

Controller operations were immediately transferred to another FAA center in Aurora, Ill., which allowed only limited departures and arrivals at the major airports.

Workers returned to the office by 3:45 p.m. ET, after FAA technicians cleared residual smoke from the radar room.

But the problem forced FAA to halt most flights heading into or out of the airports for nearly four hours.

By 5 p.m., Flightaware.com, which tracks flights nationwide, said 736 flights were canceled and 553 were delayed at O'Hare. Cancellations represented 26% of the total flights and delays 19%, according to Flightaware.

Midway had 114 cancellations and 120 delays, which each represented 15% of total flights, according to Flightaware.

United Airlines, which has a hub at O'Hare, has already announced that thunderstorms in Chicago might delay flights today. The airline offered to waive change fees for flights.

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